Multiple sequence alignment - TraesCS4B01G348500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G348500 chr4B 100.000 2960 0 0 1 2960 641892406 641889447 0.000000e+00 5467
1 TraesCS4B01G348500 chr5A 93.082 2862 94 45 135 2956 679876187 679873390 0.000000e+00 4093
2 TraesCS4B01G348500 chr5A 86.907 443 52 3 997 1436 685432310 685432749 2.650000e-135 492
3 TraesCS4B01G348500 chrUn 95.275 1566 53 16 1368 2928 292521737 292523286 0.000000e+00 2462
4 TraesCS4B01G348500 chrUn 92.346 1411 42 24 55 1452 365430966 365429609 0.000000e+00 1947
5 TraesCS4B01G348500 chr4D 85.396 493 55 13 997 1473 502396610 502397101 2.050000e-136 496
6 TraesCS4B01G348500 chr6D 88.604 351 36 3 1093 1441 342472984 342472636 9.810000e-115 424
7 TraesCS4B01G348500 chr6A 88.319 351 37 3 1093 1441 482620206 482619858 4.560000e-113 418
8 TraesCS4B01G348500 chr2D 87.432 366 42 4 1078 1440 500362649 500363013 4.560000e-113 418
9 TraesCS4B01G348500 chr6B 88.034 351 38 3 1093 1441 516880239 516879891 2.120000e-111 412
10 TraesCS4B01G348500 chr2B 86.885 366 44 4 1078 1440 588067385 588067749 9.880000e-110 407
11 TraesCS4B01G348500 chr5D 91.209 91 8 0 90 180 332797946 332797856 1.110000e-24 124


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G348500 chr4B 641889447 641892406 2959 True 5467 5467 100.000 1 2960 1 chr4B.!!$R1 2959
1 TraesCS4B01G348500 chr5A 679873390 679876187 2797 True 4093 4093 93.082 135 2956 1 chr5A.!!$R1 2821
2 TraesCS4B01G348500 chrUn 292521737 292523286 1549 False 2462 2462 95.275 1368 2928 1 chrUn.!!$F1 1560
3 TraesCS4B01G348500 chrUn 365429609 365430966 1357 True 1947 1947 92.346 55 1452 1 chrUn.!!$R1 1397

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
659 684 0.250513 CCACCCTTCTTCCTCCTTCG 59.749 60.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2282 1.367659 TTTTTGTTGTTGCTGCTGCC 58.632 45.0 13.47 0.0 38.71 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.183014 CCACTTGGGTTAAACTCAACTTC 57.817 43.478 0.00 0.00 32.80 3.01
44 45 4.642885 CCACTTGGGTTAAACTCAACTTCA 59.357 41.667 0.00 0.00 32.80 3.02
45 46 5.301805 CCACTTGGGTTAAACTCAACTTCAT 59.698 40.000 0.00 0.00 32.80 2.57
46 47 6.488683 CCACTTGGGTTAAACTCAACTTCATA 59.511 38.462 0.00 0.00 32.80 2.15
47 48 7.360361 CACTTGGGTTAAACTCAACTTCATAC 58.640 38.462 0.00 0.00 32.80 2.39
48 49 7.228706 CACTTGGGTTAAACTCAACTTCATACT 59.771 37.037 0.00 0.00 32.80 2.12
49 50 7.778382 ACTTGGGTTAAACTCAACTTCATACTT 59.222 33.333 0.00 0.00 32.80 2.24
50 51 7.504924 TGGGTTAAACTCAACTTCATACTTG 57.495 36.000 0.00 0.00 0.00 3.16
51 52 7.284074 TGGGTTAAACTCAACTTCATACTTGA 58.716 34.615 0.00 0.00 0.00 3.02
52 53 7.776030 TGGGTTAAACTCAACTTCATACTTGAA 59.224 33.333 0.00 0.00 39.54 2.69
53 54 8.074370 GGGTTAAACTCAACTTCATACTTGAAC 58.926 37.037 0.00 0.00 36.94 3.18
61 62 9.173939 CTCAACTTCATACTTGAACAATCAAAC 57.826 33.333 0.00 0.00 44.64 2.93
75 76 7.882791 TGAACAATCAAACAGTAGTCCATACAT 59.117 33.333 0.00 0.00 32.63 2.29
76 77 9.378551 GAACAATCAAACAGTAGTCCATACATA 57.621 33.333 0.00 0.00 36.79 2.29
77 78 8.718102 ACAATCAAACAGTAGTCCATACATAC 57.282 34.615 0.00 0.00 36.79 2.39
79 80 9.161629 CAATCAAACAGTAGTCCATACATACAA 57.838 33.333 0.00 0.00 36.79 2.41
81 82 8.542497 TCAAACAGTAGTCCATACATACAAAC 57.458 34.615 0.00 0.00 36.79 2.93
83 84 7.900782 AACAGTAGTCCATACATACAAACAC 57.099 36.000 0.00 0.00 36.79 3.32
88 89 5.616270 AGTCCATACATACAAACACACACA 58.384 37.500 0.00 0.00 0.00 3.72
89 90 5.468746 AGTCCATACATACAAACACACACAC 59.531 40.000 0.00 0.00 0.00 3.82
90 91 5.237561 GTCCATACATACAAACACACACACA 59.762 40.000 0.00 0.00 0.00 3.72
91 92 6.000840 TCCATACATACAAACACACACACAT 58.999 36.000 0.00 0.00 0.00 3.21
92 93 7.118535 GTCCATACATACAAACACACACACATA 59.881 37.037 0.00 0.00 0.00 2.29
93 94 7.118535 TCCATACATACAAACACACACACATAC 59.881 37.037 0.00 0.00 0.00 2.39
118 119 8.923609 CATACACAAACAAATTATGTATGCCA 57.076 30.769 9.12 0.00 43.47 4.92
119 120 9.022915 CATACACAAACAAATTATGTATGCCAG 57.977 33.333 9.12 0.00 43.47 4.85
120 121 6.991938 ACACAAACAAATTATGTATGCCAGT 58.008 32.000 0.00 0.00 42.99 4.00
122 123 8.580720 ACACAAACAAATTATGTATGCCAGTAA 58.419 29.630 0.00 0.00 42.99 2.24
123 124 9.585099 CACAAACAAATTATGTATGCCAGTAAT 57.415 29.630 0.00 0.00 42.99 1.89
157 158 7.218963 GCTAGCATAAAATACAGCTGTTTTGAC 59.781 37.037 27.06 13.16 37.94 3.18
239 240 3.717707 TCATCTGCCTAACTCGCATAAC 58.282 45.455 0.00 0.00 35.25 1.89
380 395 5.473504 CCTCTCCTTTAAAAAGCAAGCTACA 59.526 40.000 0.00 0.00 34.69 2.74
574 593 1.773653 AGCCTCATCTCCATTTCTCCC 59.226 52.381 0.00 0.00 0.00 4.30
657 682 1.918957 CATCCACCCTTCTTCCTCCTT 59.081 52.381 0.00 0.00 0.00 3.36
659 684 0.250513 CCACCCTTCTTCCTCCTTCG 59.749 60.000 0.00 0.00 0.00 3.79
661 686 0.545548 ACCCTTCTTCCTCCTTCGCT 60.546 55.000 0.00 0.00 0.00 4.93
670 707 1.190643 CCTCCTTCGCTTCCTCTTCT 58.809 55.000 0.00 0.00 0.00 2.85
679 716 1.948144 GCTTCCTCTTCTTGCCTGGAC 60.948 57.143 0.00 0.00 0.00 4.02
725 762 1.965754 GCAGATCGAGCTGTTCCCCT 61.966 60.000 29.48 0.00 38.17 4.79
751 788 1.625818 CTAGCCAGTTCCACAGGTTCT 59.374 52.381 0.00 0.00 0.00 3.01
752 789 0.398318 AGCCAGTTCCACAGGTTCTC 59.602 55.000 0.00 0.00 0.00 2.87
753 790 0.606673 GCCAGTTCCACAGGTTCTCC 60.607 60.000 0.00 0.00 0.00 3.71
754 791 1.059913 CCAGTTCCACAGGTTCTCCT 58.940 55.000 0.00 0.00 46.37 3.69
792 829 5.278512 GGCCGAGAATTCTAAATTCCAATCC 60.279 44.000 8.25 3.40 0.00 3.01
812 849 3.052186 TCCCCCAAGCTAGCCAAATATTT 60.052 43.478 12.13 0.00 0.00 1.40
964 1001 0.990818 GGAAGGGAGGAAGGAGGCAT 60.991 60.000 0.00 0.00 0.00 4.40
965 1002 0.472044 GAAGGGAGGAAGGAGGCATC 59.528 60.000 0.00 0.00 0.00 3.91
966 1003 0.253347 AAGGGAGGAAGGAGGCATCA 60.253 55.000 0.00 0.00 0.00 3.07
998 1035 2.415010 CTCTCCTCCATCGGTGCG 59.585 66.667 0.00 0.00 0.00 5.34
1029 1066 2.440980 GCAATCAGGGCCTCCACC 60.441 66.667 0.95 0.00 34.83 4.61
1210 1247 0.524862 GAAGTACTTCCCGCTCGACA 59.475 55.000 22.74 0.00 33.64 4.35
1561 1598 0.250513 GATGTTCCTCCAGGCGACTT 59.749 55.000 0.00 0.00 40.21 3.01
1563 1600 1.079057 GTTCCTCCAGGCGACTTCC 60.079 63.158 0.00 0.00 40.21 3.46
1596 1633 0.955428 ACGACTACGACGCCTACCAA 60.955 55.000 0.00 0.00 42.66 3.67
1683 1720 4.328025 TACCAGCCGCAGCAGCAA 62.328 61.111 2.79 0.00 43.56 3.91
1700 1737 0.965363 CAATACCACCACCAGCACCC 60.965 60.000 0.00 0.00 0.00 4.61
2100 2137 1.198178 GAAGTAAACAAATGCGGCGGA 59.802 47.619 9.78 6.17 0.00 5.54
2242 2282 4.675114 ACGAAAAGAACAATTTAAGCAGCG 59.325 37.500 0.00 0.00 0.00 5.18
2321 2372 2.756760 GCTCTGATTTGCATTCCTTCCA 59.243 45.455 0.00 0.00 0.00 3.53
2405 2456 5.515106 TCATTTGGGGACTTAAATACAGGG 58.485 41.667 0.00 0.00 0.00 4.45
2414 2465 8.638873 GGGGACTTAAATACAGGGAAATTATTG 58.361 37.037 0.00 0.00 0.00 1.90
2415 2466 9.197306 GGGACTTAAATACAGGGAAATTATTGT 57.803 33.333 0.00 0.00 0.00 2.71
2549 2600 4.307032 ACATGCAAGTATCTTGGAGGTT 57.693 40.909 13.51 1.83 31.01 3.50
2562 2613 2.170166 TGGAGGTTGGATGCAATGTTC 58.830 47.619 1.94 1.64 0.00 3.18
2850 2902 2.053865 GCCTGCCTGCCTGCAATTA 61.054 57.895 0.00 0.00 41.51 1.40
2868 2920 9.603298 CTGCAATTACATACATTCATACACATC 57.397 33.333 0.00 0.00 0.00 3.06
2888 2940 3.948126 TCCATCTCTCCCTCTCTCTCTA 58.052 50.000 0.00 0.00 0.00 2.43
2889 2941 3.650942 TCCATCTCTCCCTCTCTCTCTAC 59.349 52.174 0.00 0.00 0.00 2.59
2890 2942 3.557054 CCATCTCTCCCTCTCTCTCTACG 60.557 56.522 0.00 0.00 0.00 3.51
2927 2987 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
2928 2988 4.078922 TCTCTCTCTCTCTCTCTCTCTCCT 60.079 50.000 0.00 0.00 0.00 3.69
2930 2990 4.078922 TCTCTCTCTCTCTCTCTCTCCTCT 60.079 50.000 0.00 0.00 0.00 3.69
2931 2991 3.963374 TCTCTCTCTCTCTCTCTCCTCTG 59.037 52.174 0.00 0.00 0.00 3.35
2932 2992 2.435805 TCTCTCTCTCTCTCTCCTCTGC 59.564 54.545 0.00 0.00 0.00 4.26
2935 2995 2.171237 CTCTCTCTCTCTCCTCTGCTCA 59.829 54.545 0.00 0.00 0.00 4.26
2937 2997 3.973305 TCTCTCTCTCTCCTCTGCTCATA 59.027 47.826 0.00 0.00 0.00 2.15
2938 2998 4.598807 TCTCTCTCTCTCCTCTGCTCATAT 59.401 45.833 0.00 0.00 0.00 1.78
2939 2999 5.784906 TCTCTCTCTCTCCTCTGCTCATATA 59.215 44.000 0.00 0.00 0.00 0.86
2940 3000 6.444816 TCTCTCTCTCTCCTCTGCTCATATAT 59.555 42.308 0.00 0.00 0.00 0.86
2941 3001 7.623278 TCTCTCTCTCTCCTCTGCTCATATATA 59.377 40.741 0.00 0.00 0.00 0.86
2943 3003 7.402941 TCTCTCTCTCCTCTGCTCATATATACT 59.597 40.741 0.00 0.00 0.00 2.12
2944 3004 7.564793 TCTCTCTCCTCTGCTCATATATACTC 58.435 42.308 0.00 0.00 0.00 2.59
2945 3005 7.402941 TCTCTCTCCTCTGCTCATATATACTCT 59.597 40.741 0.00 0.00 0.00 3.24
2947 3007 7.402941 TCTCTCCTCTGCTCATATATACTCTCT 59.597 40.741 0.00 0.00 0.00 3.10
2948 3008 7.564793 TCTCCTCTGCTCATATATACTCTCTC 58.435 42.308 0.00 0.00 0.00 3.20
2949 3009 7.402941 TCTCCTCTGCTCATATATACTCTCTCT 59.597 40.741 0.00 0.00 0.00 3.10
2950 3010 7.564793 TCCTCTGCTCATATATACTCTCTCTC 58.435 42.308 0.00 0.00 0.00 3.20
2951 3011 7.402941 TCCTCTGCTCATATATACTCTCTCTCT 59.597 40.741 0.00 0.00 0.00 3.10
2952 3012 7.712639 CCTCTGCTCATATATACTCTCTCTCTC 59.287 44.444 0.00 0.00 0.00 3.20
2953 3013 8.379428 TCTGCTCATATATACTCTCTCTCTCT 57.621 38.462 0.00 0.00 0.00 3.10
2954 3014 8.478066 TCTGCTCATATATACTCTCTCTCTCTC 58.522 40.741 0.00 0.00 0.00 3.20
2955 3015 7.564793 TGCTCATATATACTCTCTCTCTCTCC 58.435 42.308 0.00 0.00 0.00 3.71
2956 3016 7.181845 TGCTCATATATACTCTCTCTCTCTCCA 59.818 40.741 0.00 0.00 0.00 3.86
2957 3017 7.495934 GCTCATATATACTCTCTCTCTCTCCAC 59.504 44.444 0.00 0.00 0.00 4.02
2958 3018 8.442660 TCATATATACTCTCTCTCTCTCCACA 57.557 38.462 0.00 0.00 0.00 4.17
2959 3019 8.539544 TCATATATACTCTCTCTCTCTCCACAG 58.460 40.741 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.940657 GCTAGTTAGCTGCATCAAGTG 57.059 47.619 1.02 0.00 45.62 3.16
21 22 4.642885 TGAAGTTGAGTTTAACCCAAGTGG 59.357 41.667 0.58 0.00 41.37 4.00
22 23 5.828299 TGAAGTTGAGTTTAACCCAAGTG 57.172 39.130 0.58 0.00 0.00 3.16
23 24 7.287810 AGTATGAAGTTGAGTTTAACCCAAGT 58.712 34.615 0.00 0.00 0.00 3.16
24 25 7.745620 AGTATGAAGTTGAGTTTAACCCAAG 57.254 36.000 0.00 0.00 0.00 3.61
25 26 7.776030 TCAAGTATGAAGTTGAGTTTAACCCAA 59.224 33.333 0.00 0.00 39.59 4.12
26 27 7.284074 TCAAGTATGAAGTTGAGTTTAACCCA 58.716 34.615 0.00 0.00 39.59 4.51
27 28 7.739498 TCAAGTATGAAGTTGAGTTTAACCC 57.261 36.000 0.00 0.00 39.59 4.11
28 29 8.617809 TGTTCAAGTATGAAGTTGAGTTTAACC 58.382 33.333 0.00 0.00 45.88 2.85
29 30 9.997482 TTGTTCAAGTATGAAGTTGAGTTTAAC 57.003 29.630 0.00 0.00 45.88 2.01
32 33 8.902806 TGATTGTTCAAGTATGAAGTTGAGTTT 58.097 29.630 0.00 0.00 45.88 2.66
33 34 8.450578 TGATTGTTCAAGTATGAAGTTGAGTT 57.549 30.769 0.00 0.00 45.88 3.01
34 35 8.450578 TTGATTGTTCAAGTATGAAGTTGAGT 57.549 30.769 0.00 0.00 45.88 3.41
35 36 9.173939 GTTTGATTGTTCAAGTATGAAGTTGAG 57.826 33.333 0.00 0.00 45.88 3.02
36 37 8.681806 TGTTTGATTGTTCAAGTATGAAGTTGA 58.318 29.630 0.00 0.00 45.88 3.18
37 38 8.854979 TGTTTGATTGTTCAAGTATGAAGTTG 57.145 30.769 0.00 0.00 45.88 3.16
38 39 8.686334 ACTGTTTGATTGTTCAAGTATGAAGTT 58.314 29.630 0.00 0.00 45.88 2.66
39 40 8.225603 ACTGTTTGATTGTTCAAGTATGAAGT 57.774 30.769 0.00 0.00 45.88 3.01
40 41 9.817365 CTACTGTTTGATTGTTCAAGTATGAAG 57.183 33.333 0.00 0.00 45.88 3.02
41 42 9.337396 ACTACTGTTTGATTGTTCAAGTATGAA 57.663 29.630 0.00 0.00 42.60 2.57
42 43 8.902540 ACTACTGTTTGATTGTTCAAGTATGA 57.097 30.769 0.00 0.00 42.60 2.15
43 44 8.230486 GGACTACTGTTTGATTGTTCAAGTATG 58.770 37.037 0.00 0.00 42.60 2.39
44 45 7.936847 TGGACTACTGTTTGATTGTTCAAGTAT 59.063 33.333 0.00 0.00 42.60 2.12
45 46 7.276658 TGGACTACTGTTTGATTGTTCAAGTA 58.723 34.615 0.00 0.00 42.60 2.24
46 47 6.119536 TGGACTACTGTTTGATTGTTCAAGT 58.880 36.000 0.00 0.00 42.60 3.16
47 48 6.618287 TGGACTACTGTTTGATTGTTCAAG 57.382 37.500 0.00 0.00 42.60 3.02
48 49 7.717436 TGTATGGACTACTGTTTGATTGTTCAA 59.283 33.333 0.00 0.00 40.09 2.69
49 50 7.220740 TGTATGGACTACTGTTTGATTGTTCA 58.779 34.615 0.00 0.00 0.00 3.18
50 51 7.667043 TGTATGGACTACTGTTTGATTGTTC 57.333 36.000 0.00 0.00 0.00 3.18
51 52 9.162764 GTATGTATGGACTACTGTTTGATTGTT 57.837 33.333 0.00 0.00 0.00 2.83
52 53 8.318412 TGTATGTATGGACTACTGTTTGATTGT 58.682 33.333 0.00 0.00 0.00 2.71
53 54 8.716646 TGTATGTATGGACTACTGTTTGATTG 57.283 34.615 0.00 0.00 0.00 2.67
61 62 6.871492 TGTGTGTTTGTATGTATGGACTACTG 59.129 38.462 0.00 0.00 0.00 2.74
75 76 6.761714 TGTGTATGTATGTGTGTGTGTTTGTA 59.238 34.615 0.00 0.00 0.00 2.41
76 77 5.586643 TGTGTATGTATGTGTGTGTGTTTGT 59.413 36.000 0.00 0.00 0.00 2.83
77 78 6.054035 TGTGTATGTATGTGTGTGTGTTTG 57.946 37.500 0.00 0.00 0.00 2.93
79 80 6.094186 TGTTTGTGTATGTATGTGTGTGTGTT 59.906 34.615 0.00 0.00 0.00 3.32
81 82 6.054035 TGTTTGTGTATGTATGTGTGTGTG 57.946 37.500 0.00 0.00 0.00 3.82
83 84 8.572828 AATTTGTTTGTGTATGTATGTGTGTG 57.427 30.769 0.00 0.00 0.00 3.82
111 112 7.981789 TGCTAGCTCATATTATTACTGGCATAC 59.018 37.037 17.23 0.00 36.82 2.39
112 113 8.078060 TGCTAGCTCATATTATTACTGGCATA 57.922 34.615 17.23 0.00 36.82 3.14
115 116 8.948631 TTATGCTAGCTCATATTATTACTGGC 57.051 34.615 17.23 0.00 32.89 4.85
124 125 8.944029 CAGCTGTATTTTATGCTAGCTCATATT 58.056 33.333 17.23 0.00 39.29 1.28
125 126 8.099537 ACAGCTGTATTTTATGCTAGCTCATAT 58.900 33.333 20.16 3.23 39.29 1.78
126 127 7.445121 ACAGCTGTATTTTATGCTAGCTCATA 58.555 34.615 20.16 3.32 39.29 2.15
127 128 6.294473 ACAGCTGTATTTTATGCTAGCTCAT 58.706 36.000 20.16 4.41 39.29 2.90
128 129 5.674525 ACAGCTGTATTTTATGCTAGCTCA 58.325 37.500 20.16 0.00 39.29 4.26
129 130 6.610741 AACAGCTGTATTTTATGCTAGCTC 57.389 37.500 22.01 0.00 39.29 4.09
130 131 7.121168 TCAAAACAGCTGTATTTTATGCTAGCT 59.879 33.333 22.01 4.07 41.76 3.32
131 132 7.218963 GTCAAAACAGCTGTATTTTATGCTAGC 59.781 37.037 22.01 8.10 34.10 3.42
132 133 8.236586 TGTCAAAACAGCTGTATTTTATGCTAG 58.763 33.333 22.01 5.25 34.10 3.42
133 134 8.020819 GTGTCAAAACAGCTGTATTTTATGCTA 58.979 33.333 22.01 1.44 35.64 3.49
148 149 5.240623 TGCTTATTGGTAGGTGTCAAAACAG 59.759 40.000 0.00 0.00 35.64 3.16
157 158 3.633525 ACATGCATGCTTATTGGTAGGTG 59.366 43.478 26.53 0.00 0.00 4.00
239 240 1.203523 GTCATGCTATAGGGAGAGCCG 59.796 57.143 1.04 0.00 39.28 5.52
327 328 1.341482 TGGGGTGTGAGAGCTAGAGAG 60.341 57.143 0.00 0.00 0.00 3.20
328 329 0.704664 TGGGGTGTGAGAGCTAGAGA 59.295 55.000 0.00 0.00 0.00 3.10
329 330 1.686052 GATGGGGTGTGAGAGCTAGAG 59.314 57.143 0.00 0.00 0.00 2.43
330 331 1.689575 GGATGGGGTGTGAGAGCTAGA 60.690 57.143 0.00 0.00 0.00 2.43
331 332 0.755686 GGATGGGGTGTGAGAGCTAG 59.244 60.000 0.00 0.00 0.00 3.42
380 395 3.356290 GGAAAGAGTGGGCACAATACAT 58.644 45.455 0.00 0.00 0.00 2.29
467 482 5.335426 GCTTAGCTAGTGTGTGTAGTGTGTA 60.335 44.000 0.00 0.00 0.00 2.90
574 593 2.040359 GGAGGAAGGGGAGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
657 682 0.036952 CAGGCAAGAAGAGGAAGCGA 60.037 55.000 0.00 0.00 0.00 4.93
659 684 0.326264 TCCAGGCAAGAAGAGGAAGC 59.674 55.000 0.00 0.00 0.00 3.86
661 686 0.693049 GGTCCAGGCAAGAAGAGGAA 59.307 55.000 0.00 0.00 0.00 3.36
670 707 2.005606 TTCTTGCAGGGTCCAGGCAA 62.006 55.000 15.99 15.99 44.50 4.52
679 716 0.829182 AGCTTGGGTTTCTTGCAGGG 60.829 55.000 0.00 0.00 0.00 4.45
725 762 1.276622 GTGGAACTGGCTAGGAAGGA 58.723 55.000 0.85 0.00 0.00 3.36
751 788 2.516448 CCGACTGGAATAGGCAGGA 58.484 57.895 0.00 0.00 37.49 3.86
756 793 1.107538 TCTCGGCCGACTGGAATAGG 61.108 60.000 27.28 11.66 37.49 2.57
757 794 0.744874 TTCTCGGCCGACTGGAATAG 59.255 55.000 27.28 12.49 37.49 1.73
758 795 1.410004 ATTCTCGGCCGACTGGAATA 58.590 50.000 29.43 12.89 37.49 1.75
759 796 0.541863 AATTCTCGGCCGACTGGAAT 59.458 50.000 26.71 26.71 37.49 3.01
760 797 0.108329 GAATTCTCGGCCGACTGGAA 60.108 55.000 27.28 25.89 37.49 3.53
761 798 0.970937 AGAATTCTCGGCCGACTGGA 60.971 55.000 27.28 18.29 37.49 3.86
792 829 6.478512 TTAAAATATTTGGCTAGCTTGGGG 57.521 37.500 15.72 0.00 0.00 4.96
812 849 4.729881 AGTATAGGATTTGGGTGGGCTTAA 59.270 41.667 0.00 0.00 0.00 1.85
964 1001 4.982956 AGGAGAGGTAGGTTAGGTAGATGA 59.017 45.833 0.00 0.00 0.00 2.92
965 1002 5.318630 GAGGAGAGGTAGGTTAGGTAGATG 58.681 50.000 0.00 0.00 0.00 2.90
966 1003 4.354686 GGAGGAGAGGTAGGTTAGGTAGAT 59.645 50.000 0.00 0.00 0.00 1.98
998 1035 0.099436 GATTGCGGTGAACTCCATGC 59.901 55.000 0.00 0.00 0.00 4.06
1063 1100 2.426023 GGCCTTATGATCCGCCGT 59.574 61.111 0.00 0.00 0.00 5.68
1210 1247 1.913762 CCTTGTCGGTGGAGGAGGT 60.914 63.158 0.00 0.00 32.11 3.85
1467 1504 2.273776 GAGGGGAGAGCAAAGCCC 59.726 66.667 0.00 0.00 41.28 5.19
1561 1598 4.828296 GTAGAGGGTCGCCGGGGA 62.828 72.222 18.63 18.63 0.00 4.81
1573 1610 1.520590 GTAGGCGTCGTAGTCGTAGAG 59.479 57.143 0.00 0.00 41.79 2.43
1683 1720 2.966732 CGGGTGCTGGTGGTGGTAT 61.967 63.158 0.00 0.00 0.00 2.73
1700 1737 3.343788 GACTCCAGGACCAGCGACG 62.344 68.421 0.00 0.00 0.00 5.12
1978 2015 2.362736 AGTAGTAGTGGATCGTGCGAA 58.637 47.619 0.00 0.00 0.00 4.70
2242 2282 1.367659 TTTTTGTTGTTGCTGCTGCC 58.632 45.000 13.47 0.00 38.71 4.85
2321 2372 2.086610 AGCACACAAGGGGAAATTGT 57.913 45.000 0.00 0.00 41.47 2.71
2520 2571 8.382030 TCCAAGATACTTGCATGTATTGTATG 57.618 34.615 22.10 17.51 33.74 2.39
2838 2890 5.503662 TGAATGTATGTAATTGCAGGCAG 57.496 39.130 1.90 0.00 0.00 4.85
2839 2891 6.545298 TGTATGAATGTATGTAATTGCAGGCA 59.455 34.615 1.90 4.05 0.00 4.75
2840 2892 6.857964 GTGTATGAATGTATGTAATTGCAGGC 59.142 38.462 1.90 0.00 0.00 4.85
2841 2893 7.929159 TGTGTATGAATGTATGTAATTGCAGG 58.071 34.615 1.90 0.00 0.00 4.85
2842 2894 9.603298 GATGTGTATGAATGTATGTAATTGCAG 57.397 33.333 1.90 0.00 0.00 4.41
2843 2895 8.567104 GGATGTGTATGAATGTATGTAATTGCA 58.433 33.333 0.00 0.00 0.00 4.08
2844 2896 8.567104 TGGATGTGTATGAATGTATGTAATTGC 58.433 33.333 0.00 0.00 0.00 3.56
2850 2902 7.971201 AGAGATGGATGTGTATGAATGTATGT 58.029 34.615 0.00 0.00 0.00 2.29
2868 2920 3.557054 CGTAGAGAGAGAGGGAGAGATGG 60.557 56.522 0.00 0.00 0.00 3.51
2888 2940 3.366396 AGAGAGAGAGAGAGAGAGACGT 58.634 50.000 0.00 0.00 0.00 4.34
2889 2941 3.634448 AGAGAGAGAGAGAGAGAGAGACG 59.366 52.174 0.00 0.00 0.00 4.18
2890 2942 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
2927 2987 8.481314 AGAGAGAGAGAGTATATATGAGCAGAG 58.519 40.741 0.00 0.00 0.00 3.35
2928 2988 8.379428 AGAGAGAGAGAGTATATATGAGCAGA 57.621 38.462 0.00 0.00 0.00 4.26
2930 2990 7.181845 TGGAGAGAGAGAGAGTATATATGAGCA 59.818 40.741 0.00 0.00 0.00 4.26
2931 2991 7.495934 GTGGAGAGAGAGAGAGTATATATGAGC 59.504 44.444 0.00 0.00 0.00 4.26
2932 2992 8.539544 TGTGGAGAGAGAGAGAGTATATATGAG 58.460 40.741 0.00 0.00 0.00 2.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.